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This page gives descriptions and links to various projects, resources and software being developed by the Purcell Lab.

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

gPLINK is a Java-based GUI for PLINK, designed to facilitate PLINK analysis, provide a simple project tracking environment and integration with the Haploview package.

An online resource for power calculation for several simple, commonly-used genetic study designs, including case/control and family-based designs. This site replaces the old UK-based host statgen.iop.kcl.ac.uk.

This tool provides a simple interface from which case/control and TDT analyses can be conducted, for the analysis of one or more samples simultaneously. A number of genetic models can be compared (e.g. multiplicative, dominant, etc); genotypic relative risks and/or population allele frequencies can be equated across samples or tested for heterogeneity.

whap is a C/C++ program for haplotype analysis. It can handle SNPs or multiallelic markers; disease or quantitative traits; unrelated individuals or family-based samples. In particular, it is possible to test nested models in a flexible manner that enables various types of conditional analysis (e.g. whether a particular haplotype can explain all the association signal at a locus, or whether a particular variant has any effects independent of the effects of correlated haplotypes). An example application of whap is described in this manuscript.

L-POP is a C/C++ program to detect population stratification in samples of unrelated individuals. It uses an approach similar in spirit to that used in STRUCTURE, except it is based on latent class analysis. The method has been described in this manuscript.

parenTDT is a C/C++ program designed to perform simple TDT-based association analysis but also incorporating information about the parental phenotypes. As shown in this manuscript, this procedure can increase power whilst retaining a considerable degree of protection against population stratification.

famtypes is a C/C++ program designed to help dealing with pedigree files. It will check the integrity of a pedigree file, break down extended families in nuclear families, select out various types of family types and produce summary statistics for the sample.

GenoCluster is a Perl script designed to perform a more aggressive clustering/calling of Sequenom genotype data; it provides a graphical interface and automatically constructs webpages that can be used to for QC tracking (MGH internal use only)

This site provides a collection of modules I created in 2001, designed to offer a gentle introduction to some of the fundamental quantitative genetic concepts in twin studies. In addition, some simple descriptions of other statistical genetic concepts such as linkage disequilibrium and maximum likelihood estimation can be found by following this the above link.

This link provides a collection of Mx (a freely available model-fitting package developed by Mike Neale, that is commonly used for modelling genetically-informative family data) scripts that accompany this manuscript.

This link provides a collection of Mx scripts that accompany this manuscript.

Most of the software provided above is in the form of C/C++ source code: to create a file that can run on your particular operating system, you will need to compile these files. This link gives some advice on this step.

This link has information for account setup, database access and other MGH-only features.